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Yes, in the exact same way as XCode 3 supports targetting older version with the current SDK: simply set the Deployment Target (yes, I know the example they give is Mac OSX but it works exactly the same on iOS).
 
Weird question there, because, it supports every iOS since the beginning.
So, u can program for 3.1.3 also in ur Xcode 4 :)
Good luck (it's matter of putting some flags in ur build config). and using non deprecated methods ;)
 
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